Jakob Wirbel was a PhD student in the lab from 2017-08-16 to 2021-10-15, later a Bridging Postdoc until 2022-04-15. He’s now doing postdoctoral work with Ami Bhatt at Stanford University.
SIAMCAT: Statistical Inference of Associations between Microbial Communities And host phenoTypes
[PREPRINT] A realistic benchmark for the identification of differentially abundant taxa in (confounded) human microbiome studies
[PREPRINT] Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson’s disease
[PREPRINT] ATF6 activation alters colonic lipid metabolism causing tumor-associated microbial adaptation
C. difficile may be overdiagnosed in adults and is a prevalent commensal in infants
Location and condition based reconstruction of colon cancer microbiome from human RNA sequencing data
Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments
Depression and fatigue in active IBD from a microbiome perspective-a Bayesian approach to faecal metagenomics
A faecal microbiota signature with high specificity for pancreatic cancer
Microbiota-dependent activation of the myeloid calcineurin-NFAT pathway inhibits B7H3- and B7H4-dependent anti-tumor immunity in colorectal cancer
Calorie restriction improves metabolic state independently of gut microbiome composition: a randomized dietary intervention trial
Identifying temporal and spatial patterns of variation from multimodal data using MEFISTO
Unravelling the collateral damage of antibiotics on gut bacteria
Commensal Clostridiales strains mediate effective anti-cancer immune response against solid tumors
Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox
Metabolic models predict bacterial passengers in colorectal cancer
Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer
Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation
Extensive transmission of microbes along the gastrointestinal tract